Fortunately these two seem to not be a threat after all. This could have turned very ugly, but the seemingly devout priest would rather serve the Miko as per divine will than abduct her as per the kindgom's orders. It's kinda cute that the warrior turned out to be a swordswoman who followed the priest because she was attracted to him, and a good thing since she's there to wrangle the guy.
As to them joining the village, it would actually work in their favor to let them, since driving them away risks information about their secret new village being leaked back to the kingdom. If they don't come back, the kingdom can just assume they were killed by monsters deep in the jungle.
Not sure how their appearance now affects the current conflict with the tribal refugees though. But the longer the main characters stay away from the village, the higher the chance the refugees will discover they took in other humans.